Fig. 2: Ramified CX3CR1⁺ capillary-associated myeloid cells are bona fide microglia.

a Electron microscopy images of capillary-associated microglia (mg) showing their cytoplasm (*), directly adjacent to blood vessels (bv) and astrocytic process (ap) in various brain regions. Microglial cell cytoplasm is psuedocolored yellow. Representative images were observed in three mice. b, c Representative projection images from a CX3CR1^GFP/+ brain showing myeloid cells (green), the vasculature (lectin in magenta) and CD206⁺ (b) or P2RY12 (c) cells (white). d, e Quantification of CD206⁺ and CD206⁻ cells (d, n = 3 mice) or P2RY12⁺ and P2RY12⁻ cells (e, n = 3 mice). f Distribution of capillary-associated microglia in the cortex (CTX), thalamus (TLM), and hippocampus (HPC) as quantified from fixed brain tissues. n = 3–5 mice. g IMARIS generated 3D reconstructed image from two-photon data of microglial somata (green) associated with the vasculature (magenta). h Distribution of capillary-associated microglia (CAMs) amongst total microglia and blood vessel (BV) volume in total brain volume. n = 6 mice. Data are presented as mean values ± SEM. ****p < 0.0001. Two-sided unpaired Student’s t test in (e).